Ca²⁺ influx is one of the critical events that trigger synaptic vesicular release, and the accumulation of residual free Ca²⁺ in synapses is also important for activity-dependent synaptic plasticity. Ca²⁺ imaging with fluorescence indicators (synthetic or genetically encoded) is a powerful approach to monitor Ca²⁺ levels in neurons and synapses. Although accumulating studies in vertebrate systems have been carried out to demonstrate the role of Ca²⁺ in synaptic transmission and plasticity, most of these studies rely on pharmacological methods to infer the molecular mechanism, with less emphasis on forward genetic analysis. The Drosophila neuromuscular junction (NMJ) is a powerful neurogenetic platform for studying synaptic transmission, because of the availability of many mutations. However, not many mutations have been analyzed with Ca²⁺ imaging. Besides, although Genetically Encoded Ca²⁺ Indicators (GECIs) including GCaMPs are increasingly popular as the tool to identify neuronal circuits activated by certain stimuli or mediating particular behaviors, the physiological and functional interpretation of neuronal Ca²⁺ transients reported by GECIs remain obscure. By expressing GCaMPs in NMJ synapses, I characterized a spectrum of genetic mutations including sodium channel alleles parats¹, parabss¹, potassium channel mutations Shaker (ShM, Sh¹²⁰), Shab³, ether-a-go-go (eag¹, eag⁴pm), and double mutant eag¹ Sh¹²⁰. Drosophila NMJs contain at least three different types of synapses, which include glutamatergic tonic motor synapse type Ib, phasic motor synapse type Is, and modulatory octopaminergic synapse type II. In this study, I found that the ion channel mutations did not uniformly alter the Ca²⁺ dynamics in type Ib, Is and II synapses. Based on genetic dissection and pharmacological analyses, I concluded that the excitability type I and type II synapses are differentially regulated by various ion channels, and that ion channels mainly influence the influx of Ca²⁺ upon membrane depolarization but not the subsequent clearance. I also attempted to interpret the significance of synaptic Ca²⁺ transients by correlating Ca²⁺ imaging with electrophysiological recordings. One important gap in the application of GCaMP indicators is its postsynaptic physiological relevance. Correlation of synaptic GCaMP Ca²⁺ transients with postsynaptic currents simultaneously recorded by focal extracellular recording indicated that Ca²⁺ transients reported by GCaMPs were slow, and did not reflect immediate synaptic transmission. Rather, the kinetics of synaptic Ca²⁺ transients was temporally correlated with short-term synaptic plasticity such as facilitation and depression. The hyperexcitable ion channel mutations Sh and parabss¹ enhanced the synaptic Ca²⁺ transient amplitudes as well as depression. Type Is synapses of hyperexcitable mutations such as eag¹ Sh¹²⁰ and parabss¹ often displayed single stimulus pulse-evoked Ca²⁺ transients, which were induced by high frequency repetitive firing of action potentials. Such Ca²⁺ transients were correlated with supernumerary peaks of postsynaptic currents. Based on the slow kinetics and the correlation with short-term plasticity, I conclude that GCaMP Ca²⁺ signals better reflect the accumulation of cytosolic residual Ca²⁺. The spontaneous Ca²⁺ waves in larval motor neurons were well correlated with high frequency nerve action potentials, suggesting that accumulation of residual Ca²⁺ occurs in larval crawling. Overall, this study provided important information about the different excitability control and Ca²⁺ clearance mechanisms in different synapses, and examined how membrane excitability controls the influx and accumulation of synaptic cytosolic residual Ca2+, as indicated by GCaMPs. Further, by correlating synaptic Ca²⁺ dynamics with electrophysiology, this study also investigated how to interpret GCaMP Ca²⁺ signals in the context of facilitation and depression, establishing a basis for an integrated approach of studying short-term synaptic plasticity from complementary physiological signals.